getPathwaysFromGenesAndCondition: Get pathways connected to genes which are differentially...
In AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Description Usage Arguments Value Author(s) Examples

Get list of pathway names that are connected to genes (via proteins which are encoded for by those genes) and which are reported as differentially expressed under a specified condition. The condition is specified as an ontology URI.

1	getPathwaysFromGenesAndCondition(condition, endpoint = "http://www.ebi.ac.uk/rdf/services/atlas/sparql")

`condition`	URI of a condition based on the EFO ontology class.
`endpoint`	The location of the SPARQL endpoint - default value is live Atlas endpoint

Returns a data frame with the following:

`pathwayname`	The name of the pathway
`pathway`	The URI identifier of the pathway
`expressionvalue`	The gene and expression for the pathway
`pvalue`	p-value of the differential expression of the gene for this pathway in this condition

James Malone, Simon Jupp

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    ###get pathways connected to genes which are differentially expressed for HeLa (efo:EFO_00011185)
    #getPathwaysFromGenesAndCondition("efo:EFO_0001185")

AtlasRDF documentation built on Nov. 17, 2017, 9:33 a.m.